In my case, this was a test target that I removed all the pods from inside my podfile (because I added pods that I later realized I did not need in that target). None of the other solutions here worked for me.
Go to the Build Phases tab in the project settings for the target that's causing trouble.
Delete the section named "Check Pods Manifest" and "Copy Pods Resources"
Inside "Link Binary With Libraries" remove libPods-YourTarget.a
In your project settings in the Info tab expand "Configurations" and set the configuration for the target to None for both debug and release. (This will fix a couple of missing file warnings)
Delete your project's derived data (Window > Projects > Delete [next to your project) and restart Xcode. Build / run target.